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Hi Anthony, > > When I used --iout, in addition to --cout, for fnirt, the --iout image > appears to register well with MNI152_T1_2mm image. > > However, this --iout image appears very different from the output image > after doing applywarp: > applywarp -v --ref=MNI152_T1_2mm --in=x1000024_roi > --warp=fnirted_x1000024_reducedFOV --out=warped_x1000024_reducedFOV these images should be identical. Could it be that you have given the wrong file as an argument to --warp above? The argument for --warp should be the output associated with --cout, not --iout. And if that is the case, could it possibly be that you are supplying the wrong file to invwarp? The file that you should pass to invwarp is the output from fnirt associated with --cout. Jesper